microbio msu exam 1

Fertility

(Fertility, F Factor) Donor plasmid that allows synthesis of a pilus in bacterial conjugation. Presence of the factor is indicated by F+, and lack of the factor is indicated by F−.

Recombinant

(Recombinant DNA technology) A technology, associated with genetic engineering, that deliberately modifies the genetic structure of an organism to create novel products, microbes, animals, plants, and viruses.

Acid-Fast Staining

This stain originated as a specific method to detect Mycobacterium tuberculosis in specimens. These bacterial cells have compounds in their outer wall that hold fast (tightly) to the dye (carbol fuchsin) used in the acid-fast stain, even when washed with a solution containing a combination of acid and alcohol. After staining, acid-fast bacteria appear pink, while non-acid-fast bacteria appear blue in color

generation/doubling time

Time required for a complete fission cycle- from parent cells to two new daughter cells. Also called doubling time.

Subculture

To make a second-generation culture from a well-established colony of organisms

Scanning Electron Microscope

To produce its images, the SEM bombards the surfaces of a whole, metal-coated specimen with electrons while scanning back and forth over it. A shower of electrons deflected from the surface is picked up with great accuracy by a detector, and the electron pattern is displayed as an image on a monitor screen

Assembly

Towards the end of the cycle, mature virus particles are constructed form the growing pool of parts

Porins

Transmembrane proteins of the outer membrane of gram-negtative cells taht permit transport off small molecules into the periplasmic space but bar the penetration of larger molecules

Transmission Electron Microscope

Transmission electron microscopes are the method of choice for viewing the detailed structure of cells and viruses. This microscope produces its image by transmitting electrons through the specimen.

Recombination

Transmission of DNA from one cell to another

Differential Stains

Use two different-colored dyes, called the primary dye and the counterstain, to distinguish between cell types or parts

Isotopes

Version of an element that is virtually identical in all chemical properties to another version except that their atoms have slightly different atomic masses

thylakoids

Vesicles of a chloroplast formed by elaborate folding of the inner membrane to form "discs." Solar energy trapped in the thylakoids is used in photosynthesis

Tropism

Virus bind to a cell surface via specific anti-receptor receptor molecules

cytopathic effect

Virus induced damage to the cell that alters its microscopic appearance

Explain the viral classification scheme based on genome

Viruses either have double stranded (linear or circular) DNA, single stranded (linear or circular) DNA, double stranded linear RNA, or single stranded linear RNA

naked viruses

Viruses that consist of only a nucleocapsid

ribosomes

a bilobed macromolecular complex that coordinates the codons of mRNA with RNA anticodons and, in doing so, constitutes the protein assembly site- it is composed of ribosomal RNA (rRNA) and protein

Pseudohyphae

a chain of yeast cells partitioned by constrictions rather than septa

Genome

a complete set of chromosomes and genes in an organism

Sarcina

a cubical packet of 8, 16, or more cells; the cellular arrangement of the genus Sarcina in the family Micrococcacea

mitochondria

a double-membrane organelle of eukaryotes that is the main site for aerobic respiration, it contains its own chromosomes and ribosomes

Operon

a genetic operational unit that regulates metabolism by controlling mRNA production. In sequence, the unit consists of a regulatory gene, inducer or repressor control sites, and structural genes

Protozoa

a group of single-celled eukaryotic organisms that feed on other cells and usually have a locomotor organelle

Microorganisms

a living thing ordinarily too small to be seen without magnification

flagellum

a long appendage used to propel an organism through a fluid environment. Flagella of bacteria and eukaryotes differ in structure.

slime layer

a lose shield around bacteria that protects them from dehydration and loss of nutrients, as well as serving in adhesion

Family

a mid-level division of organisms that groups are more closely related than previous levels. An order is divided into families

functional groups

a particular molecular combination that reacts in predictable ways and confers particular properties on a compound. Examples: —COOH, —OH, —CHO

Nomenclature

a set system for scientifically naming organisms

Coccus

a spherical shaped bacterial cell; cocci plural

Helminths

a term that designates parasitic worms such as roundworms or flatworms

asexual reproduction

a type of reproduction by which offspring arise from a single organism and inherit the genes of that only parent- it does not involve the fusion of gametes and almost never changes the number of chromosomes

State the chemical composition, structure and function of the following eukaryotic cell features: nucleus, nuclear membrane, nucleolus, RER, SER, chloroplast, mitochondria, Golgi apparatus, flagella, cilia, microtubules, ribosomes (including weight), glycocalyx- capsule and slime layer, cell wall, cell membrane, cytosol, cytoskeleton, centrosome, chromosome

a. Nucleus Repository of DNA Synthesis of RNA Membrane bound, nuclear envelope composed of two parallel membranes separated by narrow space and perforated with pores Contains chromosomes and DNA (linear, many copies) b. nuclear membrane Nuclear envelope with two doubled membranes c. nucleolus Genes for rRNA synthesis and ribosome assembly d. rough endoplasmic reticulum Transport materials; lipid synthesis Continuous with nuclear membrane Membrane bound in sacs and stacks Cistern spaces between sacs collect protein Protein quality control Ribosomes: 80s Subunits: 60s and 40s e. smooth endoplasmic reticulum Transport materials; lipid synthesis Stacks of interconnected sacs composed of phospholipid membrane Functions: site for lipid, phospholipid and sterol production; detoxification f. Chloroplast Convert the energy of sunlight into chemical energy through photosynthesis Found in algae and plant cells Outer membrane covers inner membrane folded into sacs, thylakoids, stacked into grana --stacked thylakoids of inner membrane capture light with chlorophyll Primary producers of organic nutrients for other organisms Have its own DNA and ribosomes g. Mitochondria Energy production: convert oxygen and nutrients into ATP using Krebs cycle, electron transport and oxidative phosphorylation Outer membrane and inner membrane with folds called the cristae --holds the enzymes and electron carriers of aerobic respiration Outer membrane provides the shape Inner membrane is folded and provides a large surface area h. Golgi apparatus Modifies proteins and lipids Produce CHO Modification chemicals (enzymes) are located in specific sites Sort and transport modified macromolecules --condensing vesicles fuse with cell membrane i. inclusion bodies j. Flagella-- 10x thicker than prokaryotes dynein arms move tubules over one another for an undulating motion grows from the base cilium--sheathed in an extension of the cell membrane Few, long thin 9+2 arrangment Cilia-- Numerous, short hair-like 9+2 arrangement Feeding and filtering k. Microtubules 9 pairs around the outside, 2 singles on inside Connect dynein arms Maintain cell shape, transport molecules, separate chromosomes (spindles) during cell reproduction l. ribosomes (including weight) Protein synthesis Some are scattered freely in the cytoplasm and cytoskeleton while others are associated with RER Arranged in short chains called polysomes 80S in the combination of 60S and 40S m. glycocalyx- capsule and slime layer Anchored to cell membrane via covalent bonds to proteins or lipids Made of carbs Functions: adhere to solid surfaces (biofilm formation), receptor, communications (signal to stop/repress gene making up flagneta) n. cell wall Shape and protection from osmotic pressure ( ex: balloon would pop at the bottom of the ocean if it was not in a submarine) Fungi and algae have thick rigid cell walls o. cell membrane (or cytoplasmic membrane) Bilayer of phospholipids with embedded protein molecules and sterols which provide stability Selectively permeable barrier in transport Cell to cell interaction Adhesion to surfaces Signal transduction p. Cytosol Aqueous component in which organelles and particles are suspended Can be used to assist in chemical reactions q. Cytoskeleton Within cytoplasmic matrix Allows pseudopod to form (for movement and feeding) Contains microfilaments and microtubules Anchors organelles r. Centrosome Centriole associated with dense material 2 cylindrical structures of tubulin at right angles Assists in mitosis spindle formation, positions nucleus, and one is the basal body of flagella and cilia s. Chromosome Threadlike structure of nucleic acids found in nucleus of cell Carries genetic information in the form of genes

State the chemical composition, structure and functions of prokaryotic cell structures: pili, fimbriae, flagella, actin filaments, ribosomes (including mass), capsule (slime layer), cell wall, cell membrane (cytoplasmic membrane), inclusion bodies, cytosol, nucleoid, plasmid, outer membrane (only in gram negative cells

a. pili and fimbriae -Fimbriae structure: Protein, sticky, bristle-like -Fimbriae function: attach to host target cells, move by rope-like pulling ; conduct electrical messages between cells + in biofilm by turning on/off genes -Pili structure/function: Specialized long fimbriae ; functions for genetic diversity (plasmid goes through pili into another cell) b. flagella (singular flagellum) -Structure: Filament: long, thin, helical structure composed of protein flagellin Hook: curved sheath Basal body: stack of rings (one set in gram +, additional in gram -) firmly anchored in cell wall; into cell membrane Paratrickious: multiple; Polar: single -Function: motility of cell through environment by: Run and tumble: run is CCW toward attractant, tumbles CW Energy provided by H+ flow across membrane: move along gradient to higher concentration of attractant c. actin filaments -Structure: actin proteins -Function: curl within body of cell and help maintain shape during cell enlargement d. ribosomes (including mass) -Structure: 70s, made up of RNA and proteins, spherical specks dispersed throughout cytoplasm, many are attached to cell membrane -Function: responsible for protein synthesis e. capsule or slime layer: composed of polysaccharides, polypeptides, or both Slime layer -Structure: loose shiefl of slime around cell -Function: protects from dehydration and loss of nutrients as well as serving as an adhesive Capsule: -Structure: bound more tightly to cell, thicker, more gummy consistency that gives a sticky characteristic to colonies of encapsulated cells -Function: Provides greater pathogenicity and blocks phagocytes f. cell wall -Structure: made up of peptidoglycan -Function: helps determine shape of a bacterium and gives structural support throughout changes in environment g. cell membrane (or cytoplasmic membrane) -Structure: thin, flexible sheath around cytoplasm, lipid bilayer embedded with proteins (Fluid mosaic model) -Function: Selective permeability into cell and regulation of transport of molecules, site for energy reactions, nutrient processing and synthesis h. inclusion bodies -Structure: special single-layered membranes, contain condensed, energy rich organic molecules such as glycogen -Function: store nutrients during times of nutrient abundance i. Cytosol -Structure: Dissolved ions. CHO, proteins, and lipids -Function: Nucleoid DNA tethered here j. Nucleoid -Structure: extremely long chromosome of DNA tightly coiled to fit inside cellular compartment, located in the central area of the cell -Function: carries genetic information k. Plasmid -Structure: small circular pieces of DNA that exist independently within cytoplasm -Function: carry additional genetic elements, duplicated and passed onto offspring, often carry genes with favorable traits, not necessary for survival l. outer membrane: only in gram negative cells -Structure: similar to cell membrane except that it contains a specialized type of lipopolysaccharides and lipoproteins -Function: works as an endotoxin, a receptor, and interfere with host defenses

appendages

accessory structures that sprout from the surface of bacteria. They can be divided into two major groups: those that provide motility and those that enable adhesion

Phosphate

acidic salt containing P and O that's an essential inorganic component of nucleic acids

nonsense codons

also called stop codon, series of 3 mRNA bases that signals the end of a polypeptide chain. UAA, UAG, UGA

Division

alternate term for phylum

Coccobacillus

an elongated coccus, short, thick, oval-shaped bacterial rod

ER

an intracellular network of flattened sacs of tubules with or without ribosomes on their surfaces

chloroplast

an organelle containing chlorophyll that is found in photosynthetic eukaryotes

Pathogen

any agent that infects body tissues and causes disease

Protistsa (Prototista)

any eukaryotic organism that is not an animal, plant, or fungus

Lipoproteins

any group of soluble proteins that combine with the transport fat or other lipids in the blood plasma

Pseudopods

appendages responsible for motility of protozoa

Classification

arrangement of plants and animals in taxonomic groups according to their similarities

obligate intracellular parasites

bacteria which are not free living, cannot function without some essential factors from the host. Require a specific host cell and instructs its genetic and metabolic machinery to make are release quantities of new viruses

Lophotrichous

bacteria which have a tuft of flagella at one or both poles

Bacillus

bacterial shape that is basically cylindrical (longer than it is wide)

Domain

broadest general category to which an organism can be assigned. Members share only one or a few characteristics

Bacteria

category of prokaryotes with peptidoglycan in their cell walls and a single circular chromosome

Eukaryote

cell that differs from prokaryotic cell by having a nuclear membrane, membrane bound organelles, and mitotic cell division

Palisades

characteristic bacterial arrangement resembling a row of fence posts created by cells snapping together

Phylogenetic

classification system based on evolutionary relationships, also called phyletic

Staphylococci

coccus shaped bacteria arranged in irregular clusters due to their division in several different planes

Exons

coding regions of the pre-rRNA; must be connected

Spirochetes

coiled spiral shaped bacterium that has endoflagella and flexes as it moves fimbria

Histone

compact and condense DNA into chromosomes while enhancing or preventing the expression of certain genes

inclusion bodies

compacted masses of viruses or damaged cell organelles in the nucleus and cytoplasm

Starch

composed of a-glucose polymers

Enriched Media

contains complex organic substances such as blood, serum, hemoglobin, or special growth factors that must be provided to certain species in order for them to grow.

lactose operon

control system that manages the regulation of lactose metabolism. It is composed of three DNA segments, including a regulator, a control locus, and a structural locus

Order

division of organism that follows class, increasing similarity can be seen here

Class

division of organisms that follows phylum

Symbiosis

evolutionary process through which prokaryotes came together to mutually benefit with eukaryotes

Taxonomy

formal system for organizing, classifying, and naming living things

Lysosome

found in cytoplasm containing degradative enzymes

metachromatic granules

granules contain crystals of inorganic compounds and are not enclosed by membranes. These granules stain a contrasting color (red, purple) in the presence of methylene blue dye.

Tetrads

groups of 4

helical capsids

have rod-shaped capsomers that bind together to form a series of hollow discs resembling a bracelet

Amphitrichous

having a single flagellum or a tuft of flagella at opposite poles of a microbial cell

Peritrichous

having flagella distributed over the entire cell

Fungi

heterotrophic unicellular or multicelullar eukaryotic organisms that may take the form of a larger macroscopic organism, as in the case of mushrooms, or a smaller microscopic organism, as in the case of mold/yeast

Capsule

in bacteria, the loose, gel-like covering or slime made chiefly of simple polysaccharides. This layer is protective and can be associated with virulence

Cristae

infolded inner membrane of a mitochondrion that is the site of respiratory chain and oxidative phosphorylation

Microscopic

invisible to naked eye

Endosymbiosis hypothesis

large prokaryotic structures engulfed smaller prokaryotes which began to live and reproduce inside the larger cell rather than being destroyed; as the smaller cells took permanent residence, they began performing functions for larger cell (food synthesis and oxygen use); cells evolved into a single functioning entity

Spontaneous generation

life arises from vital forces present in non-living matter

fatty acids

long chain unbranced hydrocarbon molecules with a carboxyl group (COOH) at one end that is free to bind to glycerol

Describe the structure and function of the three types of RNA

mRNA (messenger RNA) ---Carries DNA through complementary copy ---Message is in triplets called CODONS tRNA (transfer RNA) ---Read the information encoded in the mRNA and transfer the appropriate amino acid to growing polypeptides rRNA (ribosomal RNA) ---Components of ribosomes, needed for synthesis of proteins

Codon

mRNA sequence of 3 bases; each signals one amino acid or other instructions (start, stop, etc.)

Transcription

mRNA synthesis: DNA => mRNA

Oncovirus

mammalian viruses involved in the development of tumors

Stroma

matrix of chloroplast that is the site of dark reactions

Vacuoles

membrane-bounded sacs containing fluid or solid particles to be digested, excreted or stored

Lithoautotrophs

microbe that takes energy from reduced compounds of minerals

Monotrichous

microorganism that contains a single flagellum

Germ theory of disease

microorganisms are the cause of diseases, still considered fact

Viruses

microscopic, acellular agent composed of nucleic acid surrounded by a protein coat

Plankton

minute animals that float in the limnetic zone of water

Species

most specific level of organization

Identify the basic characteristics of prokaryotic cells

no nuclear membranes, no organelles, domain archaea and bacteria Genome structures: circular chromosome, DNA, plasmid Genome location: nucleoid Locomotion: flagella, cilia Attachment: cell membrane Cell wall content: peptidoglycan Ribosome location: cytoplasm Ribosome size: 70s ribosome Cell size: SMALL (1-5 um) Glycocalyx (a gel-like coating outside of the cell wall): capsules (compact) and slime layers (diffuse)

Introns

non-coding regions of the pre-rRNA transcript; these must be removed

Pleomorphism

normal variability of cell shapes in a single species; bacteria having diverse shapes are called pleomorphic

Algae

photosynthetic, plant like organisms that lack complex structure of plants. May be called single-celled or multicellular and inhabit diverse habitats

Translation

protein synthesis: mRNA => protein

Peptidoglycan

repeating framework of long glycan chains crossed linked with short peptide fragments.makes up the cell wall of most bacteria

Spirillum

rigid spiral shape and external flagella

Kingdom

second most general division, each domain is divided into kingdoms

Genus

second most specific level, a family is divided into several genera

Yeast

singled-celled budded fungi

Prokaryote

small cell lacking special structures such as nucleus and organelles. All prokaryotes are microorganisms

Organelles

small component of eukaryotic cells that is bounded by a membrane and specialized in function

Mitosis

somatic division that preserves the somatic chromosome number

Diplococci

spherical or oval shaped bacteria, typically found in pairs

Grana

stacks of chlorophyll containing thylakoids within chloroplasts

Define the structure and function in cells of lipids, triglycerides, fatty acids and cholesterol.

- Lipids: long or complex hydrophobic, carbon hydrogen chains - Triglycerides: are used as an energy storage: 3 fatty acids bound to glycerol - Fatty acid: consists of a carboxylic acid and a long hydrocarbon chain -Cholesterol- is a steroid that reinforces the structure of the cell membrane

Matrix

substance between the cristae of a mitochondrion that serves as a site for metabolic reactions

stationary phase

survival mode in which cells either stop growing or grow very slowly and the population number evens out

cytoplasmic membrane

synonym for cell membrane; a flexible layer in the cell appearing just beneath the cell wall, it is generally made of a lipid bilayer

Provided a drawing or photograph, identify the microbe's relationship to atmospheric oxygen by the appropriate term

-------Aerobes: uses gaseous oxygen for metabolism and have enzymes needed to process toxic oxygen products o Obligate: cannot grow without oxygen o Facultative: can live in oxygen but does not require it -------Anaerobes: lacks metabolic enzyme systems for using oxygen gas in respiration o Obligate: cannot tolerate any free oxygen in the immediate environment and will die if exposed to it o Aerotolerant: do not utilize oxygen gas but can survive and grow in its presence, not harmed by it -------Microaerophilic: requires small amount of oxygen 1) Obligate aerobe: only significant oxygen for growth at top of tube 2) Anaerobe: poisoned by oxygen, so only grows at bottom where oxygen is very low 3) Facultative aerobe: can grow whether there is oxygen or not, but higher density up top where there is oxygen 4) Microaerophil: does not grow much at top where there is lots of oxygen, also doesn't grow at bottom where there is no oxygen, grows best where there is a small amount of oxygen 5) aerotolerant

Describe the steps in and germination

-----Sporulation: formation of spores o Chromosome is duplicated and separated o Cell is separated into a sporangium and a forespore o Sporangium engulfs forespore for further development o Sporangium begins to actively synthesize spore layers around forespore o Cortex and outer coat layers are deposited o Spore completes maturation, sporangium begins to disintegrate o Free spore is released when dead sporangium falls away ------Germination: breaking of dormancy spores o Presence of a germination agent (usually a small organic molecule such as an amino acid or inorganic salt o Agent stimulates the formation of hydrolytic digestive enzymes by the endospore membrane o These enzymes digest the core and expose the core to water o As the core rehydrates and takes up nutrients, it begins to grow out of the endospore coats o In time is reverts to a fully active vegetative cell

Label and explain what is happening in the four stages of bacterial growth on a growth curve

--Lag phase: flat period of adjustment, enlargement; little growth --Exponential growth phase: a period of maximum growth and will continue as long as cells have adequate nutrients and a favorable environment --Stationary phase: rate of cell growth equals rate of cell death caused by depleted nutrients and O2, excretion of organic acids and pollutants --Death phase: as limiting factors intensify, cells die exponentially; waste product building

Describe the range of temperatures in which bacterial groups best replicate

-5 to 105 degrees celsius Hotter temps=higher growth rate

Explain the function of operons in bacterial genetic control

-Can have multiple ribosomes on the same RNA -Operons can be induced or repressed based on their needs. This allows for genes to be turned "off" when not needed, or "on" when favorable.

Describe the function and origins of viral envelopes and envelope proteins

-Envelope is acquired when the virus leaves the host cell -Envelope proteins are exposed proteins on the outside of the envelope, called spikes, that are essential for attachment of the virus to host cell

List the 3 interconnected pathways that lead to release of energy from glucose

-Glycolsis -Citric acid cycle (Kreb's cycle) -Oxidative phosphorylation

Compare the function of inducible and repressible operons and riboswitches

-Inducible (ex: lac operon) -Lactose turns the operon ON by activating the inducer -The binding of the lactose to the repressor protein changes its shape and causes it to fall off the operator -RNA polymerase can bind to the promoter -Structural genes are transcribed -If glucose is present--lac operon will be OFF because lactose is not present -Glucose provides more energy than lactose -Repressible (ex: arginine operon) -Normally on--making amino acids etc. -Will be turned off when the product of the pathway is no longer required -When excess arginine is present, it binds to the repressor and changes it -The repressor will then bind to the operator and block arginine synthesis -Arginine is the COREPRESSOR

Identify the parts and functions of the parts of the light microscope.

-Light bulb: energy source, light in visible wavelengths -Lamp housing filter: light from light bulb is focused here -Iris diaphragm: pulls light waves closer together, focuses them into condenser -Condenser: gathers light rays and focuses them in a single point on the specimen -Objective lens: enlarges the image of the specimen and forms the "real image" and projects it into the ocular lens -Ocular lens: forms the final level of magnification and forms the "virtual image", this is what is observed by the user

Explain how immersion oil improves resolution

-Oil has same density between glass slide and glass lens so we don't lose light waves -improves resolution by increasing numerical aperture allowing light to travel at a uniform speed -Prevents "light scatter" and once again, focuses light more closely on image

Describe the primary, secondary, tertiary and quaternary structure of proteins

-Primary structure is a series of amino acids bound in a chain. Amino acids display small charged functional groups (red symbols). -Secondary structure develops when CO - and NH -groups on adjacent amino acids form hydrogen bonds. This action folds the chain into local configurations called the alpha helix and b -pleated sheet. Most proteins have both types of secondary structures. Secondary structure is denatured by heats, acids- pH, alkaline, and some disinfecting agents. -Tertiary structure forms when portions of the secondary structure further interact by forming covalent disulfide bonds and additional interactions. From this emerges a stable three-dimensional molecule: curls, loops, dents, etc. Depending on the protein, this may be the final functional state. -Quaternary structure exists only in proteins that consist of more than one polypeptide chain. Several protein subunits come together to form functional proteins

List the characteristics of cells

-Prokaryotes: no nuclear membranes, No organelles, Domain Archaea and Bacteria, can metabolize, can grow, can reproduce, can respond to environment -Eukaryotes: have additionally a phospholipid bilayer nuclear membrane, organelles. -ALL cells: -Assume a cubical, spherical, or cylindrical shape -Contain a cell membrane which encases the cytoplasm -One or more chromosomes containing DNA -Ribosomes for protein synthesis -Exhibit highly complex chemical reactions

State the role of proteins in cellular structure and function

-Proteins dictate the structure, behavior, and special qualities of all living things -Function as enzymes, defense (antibodies), movement (flagella)

Describe the characteristics of viruses that make them different than prokaryotic and eukaryotic cells

-They aren't living, require a host to reproduce -Obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals -Super tiny, ranging from 20 nm to 450 nm -Consists of a protein shell (capsid) surrounding nucleic acid -Nucleic acid of viral genome is either DNA or RNA but not both (double stranded or single stranded) -Lack enzymes for most metabolic processes -Surface has high specificity proteins for attaching onto host cells -No protein synthesis -Multiply by taking control of host cell's genetic material and regulating the synthesis and assembly of new viruses

List the steps and enzymes involved in translation

-mRNA → protein -mRNA sequence of 3 bases is a CODON -Each codon signals one amino acid or instructions -tRNA recognizes codons and brings an amino acid (sense) or stops (antisense) -tRNA recognizes codons and brings an amino aid (sense) or stops (antisense) -rRNA directs the orderly assembly of amino acids into a peptide chain

List the steps in the Gram stain procedure

1. Application of crystal violet(purple dye)...crystal dye is going to bind to all neg. Charged parts (peptidoglycan) in bacteria cell wall, so both types of bacteria (Gram+ and Gram -) 2. Application of iodine(mordant)... iodine binds to crystal violet to give us a complex. Everything is purple 3. Alcohol wash (decolorization)...Dissolves/removes the complex. Time it and do it for short time: only thin peptidoglycan walls/neg. charged. (gram negative) should release color. + Gram positive (thick wall) color remains purple 4. Application of safranin (counterstain)... gram neg (thin wall) takes up pink dye from safranin. Gram positive is purple. Gram negative is now red/ pink.

List and explain the steps in Koch's Postulates. Recognize situations in which these requirements are not met.

1. The suspected germ is present in every case of the disease. 2. The germ is isolated and grown in pure culture 3. The germs is injected into a healthy, experimental host and causes the disease. 4. The same germ that caused the disease is re-isolated from the now diseased experimental host

Outline the steps and identify the effects of quorum sensing in biofilms

1.) Free swimming cells lose their motility and settle down onto a surface or substrate 2.) Cells synthesize an adhesive matrix that holds them tightly to the substrate 3.) When biofilm grows to a certain density (quorum), the cells release inducer molecules that can coordinate a response 4.) Enlargement of one cell to show genetic induction. Inducer molecule stimulates expression of a particular gene and synthesis of a protein product (such as an enzyme) 5.) Cells secrete their enzymes in unison to digest food particles Effects: allows the biofilm to react as a unit The biofilm can simultaneously produce large quantities of digestive enzyme or toxin--this regulation of expression account for several observations made about microbial activities

Identify the five phases of viral replication and explain what happens at each phase

1.adsorption- virus attaches to its host cell by specific binding of its spikes to cell receptors 2.penetration- virus is engulfed by the cell membrane into a vesicle or endosome and transported internally 3.uncoating- conditions within the endosome cause fusion of the vesicle membrane with the viral envelope, followed by release of the viral capsid and RNA into the cytoplasm. 4. Synthesis: Replication and protein production- under the control of viral genes, the cell synthesizes the basic components of new viruses:RNA molecules, capsomers and spikes. 5. Assembly- viral spike proteins are inserted into the cell membrane for the viral envelope, nucleocapsid is formed from RNA and capsomers. 6. Release- envelope viruses bud off of the membrane, carrying away an envelope with spikes. -virus is ready to infect others.

Pyrimidines

2 ringed nucleotides-- cytosine, thymine and uracil

Purines

3 ring nucleotides-- adenine and guanine

Glycerol

A 3-carbon alcohol, with three OH groups that serve as binding sites

Hexose

A 6-carbon sugar such as glucose and fructose

Transposon

A DNA segment with an insertion sequence at each enabling it to migrate to another plasmid , to the bacterial chromosome, or to a bacteriophage.

bacterial chromosome

A circular body in bacteria that contains the primary genetic material

Parasite

A close interaction in which one organism (the parasite) lives on or within another organism (the host), from which it obtains nutrients and receives protection. THe parasite produces some degree of harm to the host.

Biofilms

A complex aggregate of interacting microbial cells that adhere to each other and to surfaces by means of a polysaccharide matrix. They permit communication among participants, which facilitates their survival and adaptation

Pure Culture

A container growing a single species of microbe whose identity is known

Mixed Culture

A container that holds two or more easily differentiated species of microorganisms, not unlike a garden plot containing both carrots and onions.

ester bond

A covalent bond formed by reacting carboxylic acid with an OH group

Gram stain

A differential stain for bacteria useful in identification and taxonomy. Gram-positive organisms appear purple form crystal violet-mordant retention, whereas gram-negative organisms appear red after loss of crystal violet and absorbance of the safranin counterstain

death phase

A dramatic downturn in numbers occurs due to lack of nutrition, adverse environmental factors, and accumulation of wastes. A great number of cells are dying in this space

Glycocalyx

A filamentous network of carbohydrate-rich molecules that coats cells

group translocation

A form of active transport in which the substance being transported is altered during transfer across a plasma membrane

Commensalism

A form of mutualism where the members have an unequal relationship

Glycogen

A glucose polymer stored by cells

growth curve

A graphical representation of the change in population size over time. This graph has for periods known as lag phase, exponential or log phase, stationary phase, and death phase.

filament

A helical structure composed of proteins that is part of bacterial flagella

Cellulose

A long, fibrous polymer composed of B-glucose; one of the most common substances on earth.

atomic number (AN)

A measurement that reflects the number of protons in an atom of a particular element.

Parasitism

A microbe invades the sterile regions of a host and occupies its tissues and cells, causing some degree of damage

Saprobes

A microbe that decomposes organic remains from dead organisms, also known as saprophyte or saprotroph

Phototrophs

A microbe that uses sunlight for energy and CO2 as a carbon source

Anaerobe

A microorganism that grows best, or exclusively, in the absence of oxygen, and which does not use oxygen in its metabolism

Aerobe

A microorganism that lives and grows in the presence of free gaseous oxygen (O2)

Thermophile

A microorganism that thrives at a temperature of 50 degrees or higher

Psychrophile

A microorganism that thrives at low temperatures (0-20 degrees celsius), with a temperature optimum of 0-15 celsius

Barophiles

A microorganism that thrives under high pressure

Lipopolysaccharide

A molecular complex of lipid and carbohydrate found in the bacterial cell wall. The LPS of gram negative bacteria is an endotoxin with generalized pathologic effects such as fever

Pentose

A monosaccharide with 5 carbon atoms per molecule; ex: arabinose, ribose, xylose

spontaneous mutation

A mutation in the DNA caused by random mistakes in replication

missense mutation

A mutation in which a change in the DNA sequence results in a different amino acid being incorporated into a protein, with varying results

nonsense mutation

A mutation that changes an amino acid-based codon into a stop codon, leading to premature termination of a protein during translation

Back-mutation

A mutation that counteracts an earlier mutation, resulting in the restoration of the original DNA sequence.

silent mutation

A mutation that, because of the degeneracy of the genetic code, results in a nucleotide change in both the DNA and mRNA but not the resultant amino acid and thus, not the protein.

Mutation

A permanent inheritable alteration int he DNA sequence of a cell

Exponential

A phase of the growth of a colony where the number of times a factor is multiplied

quorum sensing

A phenomenon occurring among microbes in a biofilm in which the members signal each other and coordinate their functions

Agar

A polysaccharide found in seaweed and commonly used to prepare solid culture media. Liquid when heated, solid at room temperature

Chitin

A polysaccharide similar to cellulose in chemical structure

Hydrolysis

A process in which water is used to break bonds in molecules

Adsorption

A process of adhering one molecule onto the surface of another molecule

Spikes

A receptor on the surface of certain enveloped viruses that facilitate specific attachment to the host cell

cosahedron

A regular geometric figure having 20 surfaces that meet to form 20 corners.

Differential Medium

A single substrate that discriminates between groups of microorganisms on the basis of difference in their appearance due to different chemical reactions.

Endospore

A small, dormant, resistant derivative of a bacterial cell that germinates under favorable growth conditions into a vegetative cell

outer membrane

A structure made of lipids in the outer layer of the cell wall of gram-negative bacteria

Capsomers

A subunit of the virus capsid shaped as a triangle or disc

Budding

A synonym for exocytosis

Phagocytosis

A type of endocytosis in which the cell membrane actively engulfs large particles or cells into vesicles. A phagocyte is a cell that specialized for doing this

Triglycerides

A type of lipid composed of a glycerol molecule bound to 3 fatty acids

Bacteriophages

A virus that specifically infects bacteria

enveloped viruses

A virus whose nucleocapsid is enclosed by a membrane derived in part from the host cell

Chemoautotrophs

AN organism that relies upon inorganic chemicals for its energy and carbon dioxide for its carbon (also called chemolithotroph)

Photoautotrophs

AN organism that utilizes light for its energy and carbon dioxide chiefly for its carbon needs

point mutations

Addition, deletion, or substitution of single bases

facultative anaerobe

Aerobe that doesn't require oxygen for its metabolism and is capable of growth in its absence

Resolution

Also called resolving power, the capacity of an optical system to distinguish two adjacent objects or points from one another.Resolving Power (RP) =(Wavelength in light in nm) / (2x Numerical aperture of objective lens)

Microaerophile

An aerobic bacterium that requires oxygen at a concentration less than that in the atmosphere

polyribosomal complex

An assembly line for mass production of proteins composed of a chain of ribosomes involved in mRNA transcription

Special Staining

An example of a special stain are structural stains. Structural stains are used to emphasize special cell parts such as capsules, endospores, and flagella that are not revealed by conventional staining methods

frameshift mutation

An insertion or deletion mutation that changes the codon reading frame from the point of the mutation to the final codon. Almost always leads to a nonfunctional protein.

periplasmic space

An open area between the cell wall and cell membrane in the cell envolopes of bacteria. Gram negative bacteria have a more extensive space than do gram positive bacteria

Growth Factors

An organic compound such as a vitamin or amino acid that must be provided in the diet to facilitate growth. An essential nutrient.

obligate aerobe

An organism that cannot grow without oxygen

obligate anaerobe

An organism that does not use oxygen gas in metabolism and cannot survive in oxygen's presence

Chemotrophs

An organism that oxidizes compounds to feed on nutrients

induced mutations

Any mutations taht occurs as a consequence of exposure to mutagens

Identify the major branches of microbes studied in microbiology.

Archaea- can live in harsh environments, bacteria- cannot live in harsh environments, viruses, fungi, protozoa, helminths, algae, prions, parasites

Release

Assembled viruses leave their host either by lysis or exocytosis

Semisolid Media

At ordinary room temperature semisolid media exhibit a clot-like consistency because they contain an amount of solidifying agent (agar or gelatin) that thickens them but does not produce a firm substrate.

Compare the relative sizes of bacteria, fungi, single celled eukaryotes and viruses

Bacteria (15,500x), fungi (750x), viruses (100,000x), eukaryotes (3,500x) Big to small: fungi, eukaryotes, bacteria, viruses

Fastidious

Bacteria that require growth factors and complex nutrients

Describe three methods of transmission of genetic information in prokaryotes

Bacterial transformation -Chromosome fragments from a lysed cell are accepted by a recipient cell: the genetic code of the DNA fragments is acquired by the recipient -Donor and recipient cells can be unrelated -Useful tool in recombinant DNA technology Ex: Griffith Experiment -Bacterial transduction 1.) General: bacteriophage picks up bacterial DNA instead of viral DNA: DNA integrated with donor 2.) Specialized: phage DNA excised, new viral particles synthesized, recipient cell transfers DNA to a new cell Bacterial conjugation: -Direct gene transfer: one strand plasmid DNA transferred to recipient

Describe and recognize the structure of carbohydrates.

Basic structure: backbone of carbon bound to two or more hydroxyl groups, with an aldehyde or ketone at the end

cholesterol

Best-known member of a group of lipids called steroids. Cholesterol is commonly found in cell membranes and animal hormones.

Describe the development and importance of biofilms. Identify microbial behaviors that change in biofilms

Biofilms result when organisms attach to a substrate by some form of extracellular matrix that binds them together Biofilms favor microbial persistence in habitats and offer greater access to life-sustaining conditions Influence microbial activities such as adaptation to a particular habitat, content of soil and water, nutrient cycling and course of infections

Describe and compare the advantages and disadvantages of virus culture in cell culture, bird embryos, and live animals.

Bird embryo: Advantage: furnishes several embryonic tissues that readily support viral multiplication, embryo is intact and self supporting unit, environment is sterie, the embryo has its own nourishment Disadvantage: may not cause effects visible to the naked eye Cell culture: Advantage: possible to propagate most viruses, can be versatile (use many types of tissues: embryonic, fetal, adult, cancerous), specific cell line can be available for viruses with a very narrow host range, easily visible Disadvantage: the cell culture will eventually die out or mutate Live animals: Advantage: furnishes several tissues that readily support viral multiplication; if scientists don't know the specific tissue that the virus infects, they can determine the type of tissue(s) that is infected Disadvantage: controversial depending on the host

State the role of carbohydrates and peptidoglycan in cellular function and structure

Carbohydrate function: -cell structure -cellulose -bacterial and fungal cell walls -adhesive: a matrix excreted for biofilm formation -energy source Peptidoglycan: -provides the cell wall of most bacteria with the strength and stability it needs -this is a repeating framework of long glycan chains cross linked with short peptide fragments

Describe the basic structure of all amino acids and residues that make them distinct.

Carbon linked to an amine group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and variable R group that differentiates the amino acid and gives it unique qualities

Draw a diagram that demonstrates the relationship between and outcome of catabolism and anabolism

Catabolism: break down; break the bonds of molecule to RELEASE ENERGY (EXERGONIC REACTION) Anabolism: build up; form larger molecules from smaller molecules; REQUIRES ENERGY (ENDERGONIC REACTION)

persistent infections

Cells harbor viruses for a few weeks to even the rest of the host's life

Explain the function of coenzymes and cofactors

Cofactors: o are either coenzymes (organic) or metallic (inorganic) (ex: iron, copper, magnesium) o Metals activate enzymes o Help bring the active site and substrate close together o Participate directly in chemical reactions with enzyme-substrate complex Coenzymes: o Remove a chemical group from one molecule and add it to another substrate, serving as a temporary carrier

Explain competitive and non-competitive enzyme regulation

Competitive- substrate look-alike that competes with the normal substrate to bind at the same binding site Allosteric- product of the normal enzyme reaction binds to a regulatory site changing the conformation of the active side inhibiting normal binding Non competitive- inhibitor binds to the entire enzyme-substrate complex and inhibits reaction

Explain energy transfer through oxidation-reduction

Compound that loses electron is oxidized Compound that receives electron is reduced Need electron donor and acceptor Redox reactions also involve hydrogen atoms which donate the electron

neutralization

the process of combining an acid and a base until they reach a balanced proportion, with a pH value close to 7

sexual reproduction

the production of new living organisms by combining genetic information from two individuals of different types (sexes)

Selective Medium

Contains one or more agents that inhibit the growth of a certain microbe or microbes (call them A, B, and C) but not another (D). This difference favors, or selects, microbe D and allows it to grow by itself.

List the three types of chemical bonds and rank them in order of strength

Covalent: Strongest Ionic: Medium Hydrogen: Weakest

Secondary Stain

the secondary stain in Gram stain is called the counterstain, Safranin

Describe and compare the structure and function of DNA, RNA, and ATP

DNA - deoxyribonucleic acid Structure: A,T,C,G - nitrogen bases -Double helix Function: hereditary material, blueprint for proteins RNA - ribonucleic acid Structure: A,U,C,G - nitrogen bases Function: Organize protein synthesis Adenosine triphosphate (ATP) Structure: Nucleotide: adenine, ribose, three phosphates Function: Transfer and storage of energy, part of structure

Explain DNA mutation repair

DNA polymerase -Proofreads nucleotides during DNA replication Mismatch repair -Locates and repairs mismatched nitrogen bases that were not repaired by DNA polymerase Light repair -For UV light damage Excision repair -Locates and repairs incorrect sequence by removing a segment of the DNA and then adding the correct nucleotides

semiconservative replication

DNA replication, during the synthesis of new DNA strands (the daughter DNA), the parent strand template DNA is retained in the final molecule

Regulator

DNA segment that codes for a protein capable of repressing a operon

Synthesis

DNA viruses enter the host cell's nucleus and are replicated and assembled there. RNA viruses are replicated and assembled in the cytoplasm

List the steps and enzymes involved in transcription

DNA → RNA ---DNA acts as a template for a complementary mRNA ---Base pairs -C-G, G-C -A-U, A-U -URACIL INSTEAD OF THYMINE ---Need nucleotides, RNA polymerase, and energy ---Initiation -Sigma-factor bound to DNA -Helps RNA polymerase find correct spot to start -A-U rich -No primer needed for RNA polymerase--automatically recognizes start

Diagram the flow of genetic information from DNA to phenotype

DNA → RNA → protein DNA replication ---Parental double strand DNA molecule is converted to two identical daughter molecules in a semiconservative process ---Complementary bases allow one strand of the to act as a template ---Need free nucleotides and DNA polymerase

Predict a protein primary structure based on the encoding DNA sequence, including stop and start codons

DNA: 5' ATGCGCCTATGA 3' DNA: 3' TACGCGGATACT 5' mRNA 5' AUGCGCCUAUGA 3' AA: Met Arg Leu

Identify the structure of nucleotides and their pairing properties

DNA: A-T, C-G RNA: A-U, C-G -Nucleotide (make up DNA or RNA): phosphate group, nitrogenous base (A, T, C, G), pentose sugar -Bonds between nucleotides: covalent -Bonds between nitrogenous bases: hydrogen bonds + C-G harder to break because it has three hydrogen bonds whereas A-T has two

Liquid Media

Defined as water-based solutions that do not solidify at temperatures above freezing and that tend to flow freely when the container is tilted.

General Purpose Media

Designed to grow a broad spectrum of microbes that do not have special growth requirements. As a rule, these media are nonsynthetic (complex) and contain a mixture of nutrients that could support growth of a variety of bacteria and fungi.

aerotolerant anaerobe

Do not utilize oxygen gas but can survive and grow in its presence

order of bacteria

Domain--> Kingdom--> Phylum (Division)--> Class--> Order--> Family--> Genus--> Species

Compare steps in replication of dsDNA, positive and negative strand RNA viruses and retroviruses

Double strand DNA: just insert DNA into host cell and normal DNA replication follows Positive strand RNA virus: RNA contains message for translation and it goes directly to ribosome Negative strand RNA: RNA converted to positive sense message and requires RNA dependent RNA polymerase Retrovirus: RNA to cDNA incorporated into host cell chromosome, structural protein includes RNA dependent DNA polymerase (reverse transcriptase)

Explain the evolutionary history of eukaryotes and evidence that supports connection to prokaryotes

Earliest euks first evolved 2 billion years ago Eukaryotic cells evolved from prokaryotic cells through endosymbiosis

Describe the structure and function of enzymes in cells

Enzyme: -simple proteins: consist of protein -conjugated enzymes(holoenzymes): consist of protein and nonprotein molecules APOENZYME= protein portion COFACTORS: nonprotein portion Function: accelerate chemical reactions, not consumed in reaction

Compare the genetic material of eukaryotic and prokaryotic cells

Eukaryotic genetic material is in the form of linear chromosomes and wrapped around histones. Prokaryotic genetic material is in the form of a circular chromosome.

Plasmids

Extrachromosomal genetic units characterized by several features. A plasmid is a double-stranded DNA that is smaller than and replicates independently of the cell chromosome; it bears genes that are not essential for cell growth; it can bear genes that code for adaptive traits; and it is transmissible to other bacteria

Compare the locomotion of eukaryotes with cilia and flagella.

Flagella: undulating motion, "swim like" motion ; slow Cilia: back and forth, beating motion; fast

Compare the energy source, function and intended uses of the fluorescent, light and electron microscopes.

Fluorescent: Energy source- ultraviolet light source -Function- uses dyes that emit visible light when bombarded with shorter UV rays... fluorescence...able to visualize image at greater resolution -Intended use: useful in diagnosing infections - bacteria binds with fluorescences, can scan quickly for cell: allows for increased specificity and sensitivity Electron: Energy source- beam of electrons -Function- forms image with beam of electrons that can be made to travel in wavelike patterns when accelerated to high speeds. Magnification between 5,000x& 1,000,000x ; better resolution (electron waves shorter) -Intended use- allows us to see viruses and see inside...can see shape and construction of viruses Light: Energy source: light in visible wavelength -Function: Ocular lens, objective lens, condenser, Iris diaphragm, lamp housing filter, light source. Note: the lenses reverse the image and flip it upside down. -Intended use: to make something that is not visible to the naked eye (a cell for example), visible/ see it in finer detail

Explain the experiments that disproved spontaneous generation.

Francesco Redi: Placed meat in a jar and covered the jar with gauze, flies gathering at the jar could not actually touch meat and laid their eggs on the gauze, leading maggots to form on the gauze and not the meat, indicating that maggots came from flies and not from meat (a non- living matter) spontaneous generation Louis Jablot: Had two containers, one open to air and one not open to air. Only the open vessel developed organisms which he presumed entered through dust in the air Louis Pasteur: Two sterile flasks, one with a closed neck and the other with a broken neck. The flask with the broken neck was the only one to develop microorganisms

Identify the basic structural elements and size range of viruses

From 20nm to 50 nm

Based on use, classify media according to function as general purpose, selective, or differential.

General purpose- designed to grow broad spectrum of microbes that do not have special growth requirements. These media are non-synthetic (complex) & contain mixture of nutrients that can support variety of bacteria/fungi. Selective- contains one or more agents that inhibit the growth of a certain microbe(s). Favors one microbe and allows it to grow. Differential- grow several types of microorganisms but are designed to bring out visible differences among them. Variations include colony size/color, in media color changes, or in formation of gas bubbles or precipitations.

Identify the basic characteristics of eukaryotic cells

Genome structures: plasmid, linear chromosomes, histones, DNA Genome location: nucleus Locomotion: undulating flagella (moving in a smooth wave-like motion), pseudopodia cilia Attachment: cell membrane Cell wall content: cellulose, chitin Ribosome location: rough endoplasmic reticulum, cytoplasm, mitochondria, chloroplast Ribosome size: 70s (mitochondria, chloroplast), 80s ribosome (40s and 60s subunits) Cell size: LARGE (10-100um) Glycocalyx: capsule

Write and recognize appropriate microbial nomenclature to the genus and species levels.

Genus: First name, capitalized Species: Second name, lowercase Both italicized or underlined

Identify the cellular location of glycolysis, Kreb's cycle and electron transport carriers and ATP synthase

Glycolysis: cytoplasm Kreb's: mitochondrion ETC: cristae

Summarize the characteristics of Archaea and compare to prokaryotes and eukaryotes

Good in extreme temperatures Structure: Glycocalyx firmly attached Flagella: thinner, hollow, grow from base, *powered by ATP (differs from pro/euk: H+ ions) Fimbriae: barbed wire structure, hold onto solid structures in harsh conditions Cell wall: proteins + polysaccharides *(differs from pro/euk: peptidoglycan) Cell membrane: lipids w/o phosphate Ribosome: 70s ; made of rRNA, functions for protein production

Contrast the structural difference between gram negative and gram positive bacteria

Gram negative contains an outer membrane and a thinner shell of peptidoglycan

Categorize microbes based on the source of nutrient carbon

Heterotrophs: get carbon from live or dead organisms (use organic molecule made by another organism) Saprobes: nutrients from dead, decaying matter Symbiotic (get something, give something in return)/Parasites (do harm to host): nutrients from living host Autotrophs: get carbon from CO2 Lithotrophs: use minerals as carbon source

Define and calculate magnification

How large the object will appear under microscope compared to actual size Calculate: Ocular lens magnification x objective lens magnification

Explain the differences in solubility and chemical structure of hydrophobic and hydrophilic molecules.

Hydrophobic: water resistant, water insoluble. Non polar Hydrophilic: water loving, water soluble. polar

mutant strain

the subspecies of a microorganism that has undergone a mutation

Predict the effect of errors in the Gram stain procedure on resulting microscopic images

If too much decolorizer is used, gram-positive cells will lose the primary stain and be counterstained pink. If too little decolorizer is used, gram-negative cells will not lose the primary stain and will remain purple after counterstaining

Conjugation

In bacteria, the contact between donor and recipient cells associated with the transfer of genetic material such as plasmids. Can involve special (sex) pili. Also a form of sexual recombination in ciliated protozoans

Phylum

In levels of classification, third level from general to more specific. Each kingdom is divided into phyla

Transformation

In microbial genetics, the transfer of genetic material contained in "naked" DNA fragments from a donor cell to a competent recipient cell.

Okazaki fragments

In replication of DNA, a segment formed on the lagging strand where biosynthesis is conducted in a discontinuous manner as required by the DNA polymerase

Decolorization

In the Gram stain, the decolorization process is an Alcohol wash

Nucleocapsid

In viruses, the close physical combination of nucleic acid with its protective covering

List and describe the "Six I's" of microbial culture

Inoculation: medium contains nutrients but not other microbes. Use aseptic technique(medium was sterile/no bacteria on it). Use sterile inoculation loop and spread out on plate making it dilute until that one bacteria remains. Incubation: Atmosphere, temperature, time. Some like oxygen, some don't. Need optimal temp. Overtime, colony forms (many generations). Isolation: Method of separating individual microbes to achieve isolated colonies to distinguish them when studied with a microscope. Separate colonies. Inspection: consist of pure culture and mixed culture and check for contaminants..Macro and micro observation of cultures for analysis of cell type and morphology. (colony morphology, microscopic shape, staining characteristics). Information Gathering: Testing of cultures to identify and analyze biochemical and other features to provide specific data and build a profile of the microbes. (Additional tests: biochemical tests, drug susceptibility, nucleic acid analysis, antigen detection). Identification: Analyzing collected data to help support additional research.

List the input and output of the Kreb cycle

Input: CoA, NAD+, acetyl acid, 2 NAD+, ADP+P, FAD, NAD+ Output: CO2, NADH, CoA, 2 NADH, ATP, FADH, NADH, 4 c-molecules

List the inputs, outputs and 2 stages of fermentation

Inputs: glucose Outputs: ethanol, 2 CO2, 2 ATP Step 1: Step 2:

Transfection

Introduction of genetic material into an animal or plant cell using a viral or bacterial vector.

specificity

Limited to a single, precise characteristic or action

Compare the content and uses of liquid, semi-solid and solid media

Liquid: Synthetic chemical composition, general purpose, Example= Trypticase Soy Agar & blood agar. Semi-solid: Complex chemical composition, enriched purpose, Example= Chocolate agar Solid: Selective Purpose→ Example= CNA Differential Purpose→ Example=Hektoen Different culture medias because not all bacteria have same nutritional needs. Agar= liquid when heated, solid at room temp. Protein. Long temp range that it is a solid.

Predict the microbe by appropriate term which will exist at low, neutral or high pH, high and low osmotic pressure and high or low barometric pressure

Low: acidophiles (0-1 pH) Neutral: neutrophiles (5.5-8 pH) High: alkalinophiles (up to 12 ph) High osmotic pressure: osmophiles (common type: halophiles) Facultative halophiles--able to adapt to wide concentrations in solutes High barometric pressure: barophiles Low barometric pressure: barotolerant

Compare the outcome of lytic and lysogenic cycles

Lysogenic cycle: indefinite persistence of bacteriophage DNA in the host without production of virions Lytic cycle: Production of bacteriophages and it results in lysing of the bacteria

Compare the structure of macromolecules, polymers and monomers

Macromolecules: large compounds assembled from smaller subunits Monomer: one single subunit Polymer: a chain of monomers

List the elements essential for microbial growth and survival.

Macronutrients: sugars and amino acids that contain carbon, hydrogen and oxygen Micronutrients: magnesium, zinc, iron (involved in enzyme function and maintenance of protein structure)

wild type

the unmutated characteristic

exponential phase

Maximum rate of cell division during which growth is geometric in its rate of increase

mass number (MN)

Measurement that reflects the number of protons and neutrons in an atom of a particular element.

Synthetic Media

Media with a chemically defined composition are termed synthetic. Such media contain pure chemical nutrients that vary little from one source to another and have a molecular content specified by means of an exact formula.

Define metabolism

Metabolism: all chemical and physical workings of a cell

Explain the concept: microbes are ubiquitous on and in Earth.

Microbes are small and live in diverse places

Explain how microbes make life on Earth possible for other organisms.

Microbes provide 50% of atmospheric oxygen Aid in decomposition Microbiome is essential for human health Microbes are the sources for many foods -Nitrogen fixing microbes -Fermentation

Capnophiles

Microbes that grew best at higher CO2 concentrations (3%-10%) that are normally present in the atmosphere.

Halophiles

Microbes that need a high concentration of salt for growth or one that tolerates high salt concentration

Methanogens

Microbes that produce methane gas

Mesophiles

Microorganisms that grow at intermediate temperatures- usually between 20-40 degrees C.

Virus

Microscopic, acellular agent composed of nucleic acid surrounded by a protein coat

Peptide

Molecule composed of short chains of amino acids, such as dipeptide, tripeptide, and a tetrapeptide

inducer molecules

Molecules that brings about or causes an effect and they accumulate as the cell population grows

Positive and Negative Staining

Most procedures involve a positive stain, in which the dye actually sticks to cells and gives them color. A negative stain, on the other hand, is just the reverse (like a photographic negative). The dye does not color the specimens but dries around its outer boundary, forming a silhouette

Calculate the bacterial population size given the starting number of cells and the number of generations

N(f)= (Ni)2^n N(f)= total number of cells in the population Ni=starting number of cells Exponent n denotes number of generation

List the inputs, outputs and 3 stages of anaerobic respiration

NO3- + NADH + H+ -----> NO2- + H2O + NAD+ 1. Glycolysis 2. Fermentation 3.

Lipid

Not soluble in polar solvents; includes triglycerides, phospholipids, steroids, and waxes

active transport

Nutrient transport method that requires carrier proteins in the membranes of the living cells and expenditure of energy

Lactose

One of the carbs commonly referred to as sugars, commonly found in milk

Fructose

One of the carbs commonly referred to as sugars, commonly in fruit sugars

Sucrose

One of the carbs commonly referred to as sugars; commonly table or cane sugar

Maltose

One of the carbs referred to as sugars; fermented sugar formed from starch

chromosomes

tightly coiled bodies within cells composed of DNA

List the input and output of glycolysis

Output: 2 pyruvates, 2 ATP, 2 NADH + H+, 2 H2O Input: glucose, 2 ATP, 2 NAD+, 4 ADP + P

Explain oxidation and reduction. Predict the effect of and tendency toward electron loss or gain.

Oxidation: loss of electrons, more positive Reduction: gain of electrons, more negative

Describe and compare the passive and energy-requiring mechanisms to transport nutrients, solutes and other molecules across the cell membrane

Passive: diffusion, osmosis, facilitated diffusion (requires carrier) ; moves with concentration gradient Active: against concentration gradient, requires ATP 1). Carrier mediated: carrier proteins move to transporter, gets released into cell 2). Group translocation: multiple molecules transported into cell, change shape from outside to inside ; cell can retain "new cell" without changing concentration gradient 3). Bulk transport endocytosis : large molecules brought in by vesicle, phagosome Phagocytosis = cell eating ; pinocytosis = cell drinking

Hyphae

tubular threads that make up filamentous fungi (branched and intertwining fibers is called mycelium)

Identify attractants that stimulate microbe motility

Phototaxic: attracted to light, usually photosynthetic cells Chemotaxic: attracted to chemicals/nutrients and repelled from harmful compounds

Categorize microbes based on the source of energy

Phototrophs: photosynthesis, light Chemotrophs: chemical/organic compounds; break bonds for energy

Describe the structure and function of transposons and plasmids

Plasmids ----Double stranded DNA ----Can replicate independently or incorporate into chromosome Transposons ----Small segment of DNA that can move from one region of a DNA molecule to another

resistance plasmids

Plasmids, typically shared among bacteria by conjugation, that provide resistance to the effects of antibiotics.

Incubation

Process involves, exposing the inoculated medium to optimal growth conditions, generally for a few hours to days. Purpose and outcome, to promote multiplication and produce the actual culture. An increase in microbe numbers will provide the higher quantities needed for further testing.

Compare the timeline for emergence of prokaryotes, single celled eukaryotes and multicellular eukaryotes.

Prokaryotic cells appeared first, then eukaryotes. Soon after, reptiles, cockroaches, termites, mammals, and humans appeared

Provided a graph of minimum, maximum and optimal growth temperatures, classify microbes by the appropriate term

Psychrophile: -5 to 18 Psychrotroph: -2 to 35 Mesophile: 15 to 45 Thermophile: 40-80 Hyperthermophile: 68-105

Interpret Gram stain images

Purple cells are gram positive and pink cells are gram negative -Gram positive have thick peptidoglycan cell walls v -Gram Negative have thin peptidoglycan cell walls

Thylakoids

vesicles of a chloroplast formed by folding of the inner membrane to form "discs"; trap solar energy to use in photosynthesis

cytopathic effects

virus-induced damage to the cell that alters its microscopic appearance

Macroscopic

visible to naked eye

Archaea

Refers to one of three domains of living organisms

Simple Stains

Require only a single dye and uncomplicated procedure

Define and calculate resolution

Resolution: the capacity to distinguish or separate two adjacent objects and depends on: -wavelength of light that forms the image along with characteristics of the objects +larger wavelength: less resolution (less detail) Resolving power(RP)= (Wavelength of light in nm)/(2 X Numerical aperture of objective lens) Visible light magnification (400nm to 750nm)

Identify the difference(s) between the structure of saturated and unsaturated fatty acids

Saturated fatty acids- all carbon single bonds, more solid Unsaturated fatty acids- one or more carbon double bond, more liquidy due to "kinks"

fimbria

Short, numerous surface appendages on some bacteria that provide adhesion but not locomotion

Describe the chemical structure of DNA

Simple makeup of nucleotide=building block -----Deoxyribose sugar, nitrogenous base, phosphate group Adenine + thymine = 2 hydrogen bonds -----Takes less energy to break Cytosine + guanine = 3 hydrogen bonds Develops a 3D structure

Identify the chemical compositions and cellular targets of simple, differential, and structural stains.

Simple stains- one dye is used; reveals shape, size, and arrangement Differential stains- use a primary stain and counterstain (Two types of stains) to distinguish cell types or parts (examples: gram stain, acid-fast stain, and endospore stain) Structural stains- reveal certain cell parts not revealed by conventional methods: capsule and flagellar stains

Svedberg units

way of characterizing ribosomes. Rate the molecular sizes of various cell parts that have been spun down and separated by molecular weight and shape in centrifuge. -S rating -heavier, more compact structures sediment faster and are assigned higher s ratings

Pilus

Small, stiff filamentous appendages in gram-negative bacteria that function in DNA exchange during bacterial conjugation

Osmotolerant

Some microbes adapt to wide concentrations in solutes

basal body

where the flagella is connected to of a bacteria; a stack of rings firmly anchored through the cell wall to the cell membrane

Determine the conclusions that would be made about the origin of life by believers in the Germ Theory and the Spontaneous Generation Theories.

Spontaneous generation theory: -Life arises from vital forces present in non-living matter ---disproven The Germ theory -currently accepted theory of disease. -It states that many diseases are caused by microorganisms.

List the conditions that lead to spore formation and germination

Sporulation: depletion of nutrients within the cell, especially amino acids- dormant stage Germination: happens in the presence of water and a specific germination agent- getting out of the dormant stage

Describe the structure and function of ATP. Explain how adding and losing phosphate generates and stores energy

Structure: Nitrogen base linked to a 5-carbon sugar (ribose) with a chain of three phosphates bonded to the ribose Function: center of a cells energy cycle; energy released activates individual subunits before they are enzymatically bonded during synthesis; used to prepare a molecule for catabolism When phosphate bonds are cleaved--energy is released During oxidative phosphorylation and substrate-level phosphorylation, ATP is formed and energy is stored

Biochemistry

Study of organic compounds produced by living things

molecular weight

Sum of all of the atomic masses of the atoms a molecule contains

Explain the causes and predict the effects of nonsense, silent and frameshift mutants

~~Mutation: a change in phenotype due to a change in genotype (DNA sequence) ~~Wild type: natural, non-mutated characteristic ~~Point mutation: addition, deletion, or substitution of a single base ~~Missense: causes change in single amino acids ~~Nonsense mutation: changes a normal codon into a stop codon ~~Silent: alters a base but does not change the amino acid ~~Frameshift: when the reading frame of the mRNA is altered ~~Back mutation: when a mutated gene reverses to its original base composition

List the components of the electron transport chain

· Complex 1,2,3, and 4 · Coenzyme Q · Cytochrome C · ATP synthase

Explain the how the structure of ATP synthase functions to generate ATP from ADP and hydrogen ions

· F0 portion: o Embedded in the membrane and can rotate like a motor to pull in protons · F1 portion: o As protons flow through the F0 portion by diffusion, the F1 compartments pull in ADP and Pi · The rotation induces a change in the 3-dimensional structure of ATP synthase · This adjustment creates a high energy bond between ADP and Pi and forms ATP · ATP synthase is then rotated back to the start position to start the next round

Provided the nutritional dependence and harm caused by a microbe to the host, define the relationship between microbe and host

· Symbioses: close associations between organisms, advantageous to at least one of the members · Mutualism: all members share benefits in relationship o Obligate: require one another to survive o Nonobligate: can be separated and live apart o Commensalism: unequal relationship, one is favored and the other is neither harmed nor helped · Parasitism: microbe invades sterile region of a host and occupies it, causing some degree of damage · Syntrophy: microbes sharing a habitat feed off substances released by other organisms · Amensalism: one member of an association produces a substance that harms or kills another

Describe the range of atmospheric composition in which microbes survive and grow

Temp, pH, o2 and co2 availability, and osmotic and barometric pressures

Operator

The DNA segment where transcription of structural genes is initiated

replication forks

The Y-shaped point on a replicating DNA molecule where the DNA polymerase is synthesizing new strands of DNA

Resolving Power

The ability to show detail

atomic mass/weight

The average of the mass numbers of all the isotopic forms for a particular element.

Plaques

The clear zone of lysed cells in tissue culture or chick embryo membrane that corresponds to the area containing viruses

Saturation

The complete occupation of the active site of a carrier protein or enzyme by the substrate

peptide bond

The covalent union between two amino acids that forms between the amine group of one and the carboxyl group of the other; the basic bond of proteins

lag phase

The early phase of population growth during which little sign of growth occurs. It is this period that readies the cells for the rapid expansion to come

Pinocytosis

The engulfment, or endocytosis, of liquids by extensions of the cell membrane

RNA polymerase

The enzyme that converts the genetic code provided by DNA into a complementary RNA molecule

host range

The limitation imposed by the characteristics of the host cell on the type of viruses that can successfully invade it

Mordant

The mordant in the Gram stain is Iodine

lagging strand

The newly forming DNA strand that is discontinuously replicated in short segments (Okazaki fragments) because the template cannot be continuously read by the DNA polymerase

leading strand

The newly forming DNA strand that is replicated in a continuous fashion without fragments because it is oriented in the correct 3′ to 5′ direction for the DNA polymerase

start codon

The nucleotide codon AUG that codes for the first amino acid in protein sequences

binary fission

The parent cell enlarges, duplicates it chromosome, and forms a central transverse septum that divides the cell into two daughter cells

lysis

The physical rupture or deterioration of a cell

Primary Stain

The primary stain in a Gram stain is Crystal Violet

Sporulation

The process of spore foramtion

Uncoating

The process of the vesicle membrane becomes uncoated following endocytosis

Exocytosis

The process that releases enveloped viruses form the membrane of the host's cytoplasm

Endocytosis

The process whereby solid and liquid materials are taken into the cell through membrane invagination and engulfment into a vesicle

Capsid

The protein covering of a virus' nucleic acid core. Capsids exhibits symmetry due to the regular arrangement of subunits called capsomeres

Repressor

The protein product of a repressor gene that combines with the operator and arrests the transcription and translation of structural genes

Isolation

The separation of microbial cells by serial dilution or mechanical dispersion on solid media to create discrete colonies. Process involves, methods for separating individual microbes and achieving isolated colonies that can be readily distinguished from one another macroscopically. Purpose and outcome, to make additional cultures from single colonies to ensure they are pure; that is, containing only a single species of microbe for further observation and testing.

Microbiology

The study of life that is too small to see without magnification

chemotaxis

The tendency of cells to move in response to a chemical gradient (toward an attractant or to avoid adverse stimuli

Transduction

The transfer of genetic material from one bacterium to another by means of a bacteriophage vector.

Anticodon

The triplet sequence in transfer RNA that is complementary to the triplet sequence of messenger RNA (the codon). ribosomal RNA

Nucleoid

The undifferentiated space or region in the cytoplasm that contains the bacterial genetic material

Uncoated

The vesicle membrane becomes altered so that the viral nucleocapsid or nucleic acid can be released into the cytoplasm

Explain the concept of host cell-virus specificity and predict the impact of this specificity on infections and virus culture.

The virus binds to a cell surface via specific anti-receptor receptor molecules so that it's able to infect a specific type of cell (HIV infects CD4 cells due to antibodies on the surface of cell). It will be more difficult to culture viruses because you need to know what kind of cell the virus infects.

Penetration

The virus penetrates the cell membrane of the host cell and deliver the viral nucleic acid to the host cell's interior

Broth

These media, termed broths, milks, or infusions, are made by dissolving various solutes in distilled water.